what happens if you
cd s000_open_brain_sanlm_+TIR_normlalized/surf
mris_register lh.sphere ../../avg_all_subjects_SD/lh.reg.template.tif lh.junk
On 07/10/2013 12:40 PM, fatma zribi wrote:
SURFACE INFO ======================================== type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE num vertices: 143704 num faces : 287404 num strips : 0 surface area: 125661 AvgVtxArea 0.874440 AvgVtxDist 1.078393 StdVtxDist 0.419625 ctr : (0.000782013, 0.000278473, -0.000354767) vertex locs : surfaceRAS talairch.xfm: 1.055 0.061 0.112 -14.422; -0.160 1.180 0.231 -36.683; -0.122 -0.333 1.316 -37.246; 0.000 0.000 0.000 1.000; surfaceRAS to talaraiched surfaceRAS: 1.055 0.061 0.112 -0.656; -0.160 1.180 0.231 -13.306; -0.122 -0.333 1.316 -39.910; 0.000 0.000 0.000 1.000; talairached surfaceRAS to surfaceRAS: 0.930 -0.067 -0.068 -2.975; 0.104 0.800 -0.149 4.763; 0.113 0.196 0.716 31.244; 0.000 0.000 0.000 1.000; volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : (-0.0000, -0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : (11.4210, 20.5397, 4.2289) file : ../mri/filled-pretess255.mgz cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:20:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs s000_open_brain_sanlm_+TIR_normlalized lh ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:21:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:26:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:26:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:28:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 mris_info creationtime 2013/07/10-16:39:42-GMT sysname Linux hostname frioul03 machine x86_64 surfacefile s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere hemicode 0 talairach_flag 0 rescale 0.000000 nvertices 143704 nfaces 287404 total_area 125660.585938 group_avg_vtxarea_loaded 0 avgvtxarea 0.874440 avgvtxdist 1.078393 stdvtxdist 0.419625 vtx0xyz 30.075546 -90.141014 -31.145763
2013/7/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
and how about: mris_info s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere On Wed, 10 Jul 2013, fatma zribi wrote: Dear Bruce, this is the result: -rwxrwxr-x 1 zribi.f scalp 5175759 Jun 21 14:57 s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere 2013/7/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Hi Fatma this not what we meant. From here please run: cd .. ls -l s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere cheers Bruce On Wed, 10 Jul 2013, fatma zribi wrote: ---------- Forwarded message ---------- From: fatma zribi <zribi.fatma@gmail.com <mailto:zribi.fatma@gmail.com>> Date: 2013/7/10 Subject: Re: [Freesurfer] Fwd: how to use mris_register? To: Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Copie1/s000_open_brain_sanlm_+TIR_normlalized$ ls -l total 704 drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 bem drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 label drwxrwxr-x 4 zribi.f scalp 4096 Jul 5 17:12 mri drwxrwxr-x 2 zribi.f scalp 4096 Jul 9 10:44 scripts drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 SD drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 src drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 stats drwxrwxr-x 6 zribi.f scalp 4096 Jul 9 10:44 surf drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 tmp drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 touch drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 trash 2013/7/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> I meant can you run it and send us the results? If we can't open the file it is not an FS issue, but something with the file system. Run ls -l with the same path that you are giving mris_register Bruce On Wed, 10 Jul 2013, fatma zribi wrote: Hi Bruce, Yes i can run ls -l in the directory 2013/7/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Hi Fatma are you sure you don't have a typo in the path? Can you run ls -l on that file? Bruce On Wed, 10 Jul 2013, fatma zribi wrote: ---------- Forwarded message ---------- From: fatma zribi <zribi.fatma@gmail.com <mailto:zribi.fatma@gmail.com>> Date: 2013/7/10 Subject: Re: [Freesurfer] how to use mris_register? To: Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Hi Bruce, Thank you very much for your help but it still don't work. mris_register s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif lh.sphere_reg $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere No such file or directory note that the file exist in the folder and i have changed the SUBJECT_DIR to the appropriate folder Thank you very much for your help with best regards, Fatma 2013/7/9 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Hi Fatma don't use the -1 flag if you are regtering to a template, only if you are registering individual surfaces to each other. You probably want the output to be named lh.sphere_reg and go in the s000/surf dir. cheers Bruce On Tue, 9 Jul 2013, fatma zribi wrote: Dear Mr, When I execute mris_register to register one subject to a template., I have this message of error: mris_register -1 s000/surf/lh.sphere avg_all_subjects_SD/lh.reg.template.tif sphere_reg treating target as a single subject's surface... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere... MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file s000/surf/lh.sphere No such file or directory note that the file exist in the specifeid SUBJECT_DIR Thank you for your help Fatma The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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